[{"type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"oa":1,"file":[{"access_level":"open_access","creator":"dernst","date_updated":"2024-02-06T13:56:15Z","relation":"main_file","file_id":"14944","checksum":"32b3788f7085cf44a84108d8faaff3ce","file_size":5942467,"success":1,"file_name":"2024_Neuron_Cheung.pdf","date_created":"2024-02-06T13:56:15Z","content_type":"application/pdf"}],"date_created":"2023-04-27T09:41:48Z","abstract":[{"lang":"eng","text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny."}],"status":"public","quality_controlled":"1","corr_author":"1","article_type":"original","day":"17","scopus_import":"1","page":"230-246.e11","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter"},{"last_name":"Krausgruber","first_name":"Thomas","full_name":"Krausgruber, Thomas"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"last_name":"Schrammel","first_name":"Martin","full_name":"Schrammel, Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d"},{"full_name":"Özgen, Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","last_name":"Özgen","first_name":"Natalie Y"},{"first_name":"Alexis","last_name":"Ivec","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","full_name":"Ivec, Alexis"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"year":"2024","doi":"10.1016/j.neuron.2023.11.009","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","month":"01","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/"}]},"ddc":["570"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","isi":1,"intvolume":"       112","file_date_updated":"2024-02-06T13:56:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Neuron","license":"https://creativecommons.org/licenses/by/4.0/","volume":112,"date_published":"2024-01-17T00:00:00Z","oa_version":"Published Version","publication_status":"published","publisher":"Elsevier","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["0896-6273"]},"citation":{"short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. 2024;112(2):230-246.e11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>","ieee":"G. T. Cheung <i>et al.</i>, “Multipotent progenitors instruct ontogeny of the superior colliculus,” <i>Neuron</i>, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>."},"department":[{"_id":"SiHi"},{"_id":"RySh"}],"pmid":1,"external_id":{"isi":["001163937900001"],"pmid":["38096816"]},"_id":"12875","date_updated":"2025-12-30T10:54:12Z","article_processing_charge":"Yes (via OA deal)","issue":"2"},{"has_accepted_license":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["38070137"]},"department":[{"_id":"SiHi"}],"pmid":1,"publication_identifier":{"issn":["2666-1667"]},"citation":{"apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>.","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024."},"article_processing_charge":"Yes (in subscription journal)","date_updated":"2025-04-15T08:23:06Z","_id":"14683","issue":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"STAR Protocols","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         5","file_date_updated":"2024-07-16T11:50:03Z","oa_version":"Published Version","ec_funded":1,"date_published":"2024-03-15T00:00:00Z","volume":5,"publisher":"Elsevier","publication_status":"published","article_number":"102771","article_type":"review","year":"2024","doi":"10.1016/j.xpro.2023.102771","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","last_name":"Cheung","first_name":"Giselle T"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"project":[{"name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","grant_number":"T01031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","day":"15","month":"03","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","ddc":["570"],"file":[{"content_type":"application/pdf","date_created":"2024-07-16T11:50:03Z","file_name":"2024_STARProtoc_Amberg.pdf","success":1,"file_size":8871807,"checksum":"3f0ee62e04bf5a44b45b035662826e95","file_id":"17260","relation":"main_file","date_updated":"2024-07-16T11:50:03Z","access_level":"open_access","creator":"dernst"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"oa":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"type":"journal_article","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"date_created":"2023-12-13T11:48:05Z","quality_controlled":"1","status":"public","corr_author":"1"},{"article_type":"original","article_number":"103157","day":"20","scopus_import":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"author":[{"orcid":"0000-0001-8457-2572","last_name":"Cheung","first_name":"Giselle T","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1016/j.xpro.2024.103157","year":"2024","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","month":"09","ddc":["570"],"type":"journal_article","file":[{"success":1,"date_created":"2025-01-09T12:12:40Z","content_type":"application/pdf","file_name":"2024_STARProtoc_Cheung.pdf","date_updated":"2025-01-09T12:12:40Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"18809","file_size":5186071,"checksum":"d8a8cdba82a394e731aa699ace1ae433"}],"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2024-06-30T22:01:04Z","abstract":[{"lang":"eng","text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1"}],"status":"public","quality_controlled":"1","corr_author":"1","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"gold","has_accepted_license":"1","citation":{"ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>.","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>"},"publication_identifier":{"eissn":["2666-1667"]},"department":[{"_id":"SiHi"}],"pmid":1,"external_id":{"pmid":["38935508"]},"_id":"17187","date_updated":"2025-12-30T10:54:11Z","article_processing_charge":"Yes","issue":"3","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","intvolume":"         5","file_date_updated":"2025-01-09T12:12:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"STAR Protocols","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":5,"date_published":"2024-09-20T00:00:00Z","ec_funded":1,"oa_version":"Published Version","APC_amount":"804 EUR","publication_status":"published","publisher":"Elsevier"},{"quality_controlled":"1","status":"public","corr_author":"1","oa":1,"file":[{"success":1,"content_type":"application/pdf","date_created":"2025-01-09T12:16:53Z","file_name":"2024_STARProtoc_Cheung2.pdf","file_id":"18810","file_size":6445556,"checksum":"464f52ecc6ec92f509552823bb82bf79","date_updated":"2025-01-09T12:16:53Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"type":"journal_article","abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"date_created":"2024-07-14T22:01:10Z","month":"09","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","ddc":["570"],"article_number":"103168","article_type":"original","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"orcid":"0000-0002-3509-1948","first_name":"Peter","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"doi":"10.1016/j.xpro.2024.103168","year":"2024","day":"20","scopus_import":"1","oa_version":"Published Version","volume":5,"date_published":"2024-09-20T00:00:00Z","publication_status":"published","publisher":"Elsevier","APC_amount":"804 EUR","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication":"STAR Protocols","file_date_updated":"2025-01-09T12:16:53Z","intvolume":"         5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-30T10:54:12Z","article_processing_charge":"Yes","_id":"17232","issue":"3","language":[{"iso":"eng"}],"OA_type":"gold","OA_place":"publisher","has_accepted_license":"1","external_id":{"pmid":["38968076"]},"publication_identifier":{"eissn":["2666-1667"]},"citation":{"apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024."},"pmid":1,"department":[{"_id":"SiHi"},{"_id":"PreCl"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781071639696"],"issn":["1064-3745"],"eissn":["1940-6029"],"isbn":["9781071639689"]},"citation":{"mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299."},"pmid":1,"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"external_id":{"pmid":["39134857"]},"_id":"17425","place":"New York, NY","date_updated":"2026-04-07T12:32:35Z","article_processing_charge":"No","edition":"1","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","alternative_title":["Methods in Molecular Biology"],"intvolume":"      2831","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Neuronal Morphogenesis","date_published":"2024-08-13T00:00:00Z","volume":2831,"oa_version":"None","publication_status":"published","publisher":"Springer Nature","day":"13","page":"283-299","scopus_import":"1","project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"author":[{"last_name":"Miranda","first_name":"Osvaldo","orcid":"0000-0001-6618-6889","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","full_name":"Miranda, Osvaldo"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","last_name":"Cheung","first_name":"Giselle T"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1007/978-1-0716-3969-6_19","year":"2024","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","month":"08","series_title":"MIMB","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20212"}]},"type":"book_chapter","acknowledged_ssus":[{"_id":"Bio"}],"date_created":"2024-08-13T12:16:41Z","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.","lang":"eng"}],"editor":[{"full_name":"Toyooka, Kazuhito","last_name":"Toyooka","first_name":"Kazuhito"}],"status":"public","quality_controlled":"1","corr_author":"1"},{"date_updated":"2026-04-14T08:34:32Z","month":"05","article_processing_charge":"No","_id":"18688","title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","related_material":{"record":[{"id":"18681","relation":"dissertation_contains","status":"public"},{"id":"18879","relation":"later_version","status":"public"}]},"OA_place":"repository","language":[{"iso":"eng"}],"project":[{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"}],"author":[{"last_name":"Watson","first_name":"Jake F.","full_name":"Watson, Jake F."},{"full_name":"Vargas-Barroso, Victor","first_name":"Victor","last_name":"Vargas-Barroso"},{"full_name":"Morse-Mora, Rebecca J.","last_name":"Morse-Mora","first_name":"Rebecca J."},{"last_name":"Navas-Olive","first_name":"Andrea","full_name":"Navas-Olive, Andrea"},{"full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","first_name":"Mojtaba"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Tomschik, Matthias","last_name":"Tomschik","first_name":"Matthias"},{"last_name":"Rössler","first_name":"Karl","full_name":"Rössler, Karl"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"year":"2024","doi":"10.1101/2024.05.02.592169","citation":{"ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).","ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>"},"day":"02","department":[{"_id":"JoDa"},{"_id":"PeJo"}],"ec_funded":1,"oa_version":"Preprint","status":"public","date_published":"2024-05-02T00:00:00Z","publication_status":"draft","corr_author":"1","acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"oa":1,"type":"preprint","abstract":[{"lang":"eng","text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits."}],"publication":"bioRxiv","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.05.02.592169"}],"date_created":"2024-12-19T11:35:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-04-14T08:34:35Z","_id":"14257","external_id":{"isi":["001065254200001"],"pmid":["37653226"]},"department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"pmid":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"citation":{"apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024."},"has_accepted_license":"1","OA_place":"publisher","OA_type":"hybrid","language":[{"iso":"eng"}],"publisher":"Springer Nature","publication_status":"published","oa_version":"Published Version","ec_funded":1,"volume":42,"date_published":"2024-07-01T00:00:00Z","publication":"Nature Biotechnology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        42","file_date_updated":"2025-01-09T07:48:01Z","isi":1,"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["570"],"related_material":{"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}],"record":[{"id":"18660","relation":"dissertation_contains","status":"deleted"},{"id":"13126","status":"public","relation":"research_data"},{"id":"18674","status":"public","relation":"dissertation_contains"}]},"month":"07","title":"Imaging brain tissue architecture across millimeter to nanometer scales","doi":"10.1038/s41587-023-01911-8","year":"2024","project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E","grant_number":"LS18-022"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"101026635","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","first_name":"Julia M","last_name":"Michalska","orcid":"0000-0003-3862-1235"},{"last_name":"Lyudchik","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","first_name":"Philipp"},{"last_name":"Korinkova","first_name":"Hana","full_name":"Korinkova, Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","first_name":"Jake","last_name":"Watson"},{"first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"first_name":"Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roessler","first_name":"Karl","full_name":"Roessler, Karl"},{"first_name":"Thomas","last_name":"Czech","full_name":"Czech, Thomas"},{"full_name":"Höftberger, Romana","last_name":"Höftberger","first_name":"Romana"},{"orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"}],"page":"1051-1064","scopus_import":"1","day":"01","article_type":"original","corr_author":"1","quality_controlled":"1","status":"public","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"date_created":"2023-09-03T22:01:15Z","file":[{"file_name":"2024_NatureBiotech_Michalska.pdf","content_type":"application/pdf","date_created":"2025-01-09T07:48:01Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","date_updated":"2025-01-09T07:48:01Z","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","file_size":26065165,"file_id":"18784"}],"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"type":"journal_article"},{"ec_funded":1,"oa_version":"Published Version","date_published":"2024-12-18T00:00:00Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"file_date_updated":"2024-12-18T14:41:53Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-14T08:34:35Z","article_processing_charge":"No","_id":"18674","language":[{"iso":"eng"}],"OA_place":"publisher","has_accepted_license":"1","publication_identifier":{"isbn":[" 978-3-99078-051-0"],"issn":["2663-337X"]},"citation":{"mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024.","ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024."},"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"status":"public","corr_author":"1","file":[{"file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","content_type":"application/pdf","date_created":"2024-12-18T14:17:34Z","success":1,"checksum":"1b42b8073e2bc09fc504da52372248c1","file_size":160536833,"file_id":"18675","relation":"main_file","access_level":"open_access","creator":"jlyudchi","date_updated":"2024-12-18T14:17:34Z"},{"file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","date_created":"2024-12-18T14:21:06Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"jlyudchi","access_level":"closed","date_updated":"2024-12-18T14:41:53Z","checksum":"b4da84624060745519723698f7ddf54b","file_size":99172203,"file_id":"18676"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa":1,"type":"dissertation","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue.","lang":"eng"}],"date_created":"2024-12-18T14:24:43Z","month":"12","title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","ddc":["004"],"related_material":{"record":[{"id":"11160","status":"public","relation":"part_of_dissertation"},{"id":"18677","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13267"},{"id":"14257","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"}],"author":[{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia"}],"doi":"10.15479/at:ista:18674","year":"2024","day":"18","page":"217"},{"doi":"10.1371/journal.pcbi.1012508","year":"2024","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"F7802","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"}],"author":[{"full_name":"Ho, Richard D.J.G.","first_name":"Richard D.J.G.","last_name":"Ho"},{"last_name":"Kishi","first_name":"Kasumi","orcid":"0000-0001-6060-4795","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi"},{"first_name":"Maciej","last_name":"Majka","full_name":"Majka, Maciej"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski"}],"scopus_import":"1","day":"14","DOAJ_listed":"1","article_number":"e1012508","article_type":"original","ddc":["570"],"related_material":{"record":[{"id":"20393","status":"public","relation":"dissertation_contains"}]},"month":"10","title":"Dynamics of morphogen source formation in a growing tissue","abstract":[{"text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.","lang":"eng"}],"date_created":"2024-10-27T23:01:45Z","file":[{"date_created":"2024-10-29T11:59:09Z","content_type":"application/pdf","file_name":"2024_PloSComBio_Ho.pdf","success":1,"file_size":3732443,"checksum":"42fa714459943cb3961b40fab8fd82c8","file_id":"18487","relation":"main_file","date_updated":"2024-10-29T11:59:09Z","access_level":"open_access","creator":"dernst"}],"oa":1,"type":"journal_article","corr_author":"1","quality_controlled":"1","status":"public","external_id":{"isi":["001331700300003"],"pmid":["39401260"]},"pmid":1,"department":[{"_id":"AnKi"}],"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"citation":{"apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., &#38; Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>","ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.","short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>, vol. 20, e1012508, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>.","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. 2024;20. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” <i>PLoS Computational Biology</i>, vol. 20. Public Library of Science, 2024.","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>."},"has_accepted_license":"1","OA_type":"gold","OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2026-04-07T12:31:58Z","_id":"18481","publication":"PLoS Computational Biology","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        20","file_date_updated":"2024-10-29T11:59:09Z","isi":1,"acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publisher":"Public Library of Science","publication_status":"published","APC_amount":"3197,23 EUR","oa_version":"Published Version","date_published":"2024-10-14T00:00:00Z","volume":20},{"ddc":["570"],"month":"02","title":"Assessing the precision of morphogen gradients in neural tube development","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord"}],"author":[{"last_name":"Zagorski","first_name":"Marcin","full_name":"Zagorski, Marcin"},{"full_name":"Brandenberg, Nathalie","last_name":"Brandenberg","first_name":"Nathalie"},{"full_name":"Lutolf, Matthias","first_name":"Matthias","last_name":"Lutolf"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna"}],"year":"2024","doi":"10.1038/s41467-024-45148-8","day":"01","DOAJ_listed":"1","scopus_import":"1","article_number":"929","article_type":"letter_note","corr_author":"1","quality_controlled":"1","status":"public","date_created":"2025-01-27T13:01:01Z","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","date_updated":"2025-01-27T13:04:03Z","checksum":"acf75f2b6fa84a64d1f590dd4a53cbf7","file_size":4723831,"file_id":"18903","file_name":"2024_NatureComm_Zagorski.pdf","content_type":"application/pdf","date_created":"2025-01-27T13:04:03Z","success":1}],"oa":1,"type":"journal_article","date_updated":"2025-12-30T10:57:08Z","article_processing_charge":"Yes","_id":"18902","external_id":{"isi":["001156218500022"],"pmid":["38302459"]},"citation":{"chicago":"Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>.","ieee":"M. Zagorski <i>et al.</i>, “Assessing the precision of morphogen gradients in neural tube development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>, vol. 15, 929, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>.","ama":"Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>","ista":"Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929.","short":"M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).","apa":"Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., &#38; Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>"},"publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"department":[{"_id":"GaTk"},{"_id":"AnKi"}],"language":[{"iso":"eng"}],"OA_type":"gold","OA_place":"publisher","has_accepted_license":"1","publication_status":"published","publisher":"Springer Nature","oa_version":"Published Version","date_published":"2024-02-01T00:00:00Z","volume":15,"publication":"Nature Communications","file_date_updated":"2025-01-27T13:04:03Z","intvolume":"        15","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"has_accepted_license":"1","language":[{"iso":"eng"}],"OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"citation":{"mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","date_updated":"2026-04-15T06:43:02Z","_id":"17133","supervisor":[{"first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2024-06-20T11:52:22Z","oa_version":"Published Version","date_published":"2024-06-11T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","doi":"10.15479/at:ista:17133","year":"2024","author":[{"first_name":"Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"page":"161","day":"11","month":"06","title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","ddc":["530"],"degree_awarded":"PhD","related_material":{"record":[{"id":"13227","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9928"},{"status":"public","relation":"part_of_dissertation","id":"8755"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"file":[{"file_id":"17137","file_size":28370759,"checksum":"258c353d47fa37ea63ea43b1e10a34a0","date_updated":"2024-06-20T11:52:22Z","creator":"fhassani","access_level":"open_access","relation":"main_file","date_created":"2024-06-12T07:53:19Z","content_type":"application/pdf","file_name":"Thesis_main_final.pdf"},{"relation":"source_file","date_updated":"2024-06-12T07:54:27Z","access_level":"closed","creator":"fhassani","file_size":445735,"checksum":"deffa5d0db88093f74812fa71520d5e1","file_id":"17138","content_type":"text/x-tex","date_created":"2024-06-12T07:54:27Z","file_name":"Thesis_main.tex"}],"oa":1,"keyword":["Quantum information","Qubits","Superconducting devices"],"type":"dissertation","abstract":[{"text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing.","lang":"eng"}],"date_created":"2024-06-11T18:20:05Z","status":"public","corr_author":"1"},{"article_processing_charge":"No","date_updated":"2026-04-15T08:51:09Z","_id":"15362","external_id":{"pmid":["38658779"],"isi":["001207703200001"]},"pmid":1,"department":[{"_id":"FyKo"}],"publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"citation":{"ieee":"M. A. Andrianova <i>et al.</i>, “Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells,” <i>European Journal of Human Genetics</i>, vol. 32. Springer Nature, pp. 837–845, 2024.","chicago":"Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>.","apa":"Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B., Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>","short":"M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur, J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L. Valle, European Journal of Human Genetics 32 (2024) 837–845.","ista":"Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 32, 837–845.","mla":"Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>, vol. 32, Springer Nature, 2024, pp. 837–45, doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>.","ama":"Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. 2024;32:837-845. doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>"},"has_accepted_license":"1","OA_type":"hybrid","OA_place":"publisher","language":[{"iso":"eng"}],"publisher":"Springer Nature","publication_status":"published","oa_version":"Published Version","ec_funded":1,"date_published":"2024-07-01T00:00:00Z","volume":32,"publication":"European Journal of Human Genetics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        32","file_date_updated":"2025-01-09T09:21:25Z","isi":1,"acknowledgement":"This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR 2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL (FK)].","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["570"],"month":"07","title":"Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells","doi":"10.1038/s41431-024-01598-8","year":"2024","project":[{"name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716"},{"_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"},{"name":"Evolutionary analysis of gene regulation","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","grant_number":"I05127"}],"author":[{"full_name":"Andrianova, Maria A.","last_name":"Andrianova","first_name":"Maria A."},{"last_name":"Seplyarskiy","first_name":"Vladimir B.","full_name":"Seplyarskiy, Vladimir B."},{"last_name":"Terradas","first_name":"Mariona","full_name":"Terradas, Mariona"},{"first_name":"Ana Beatriz","last_name":"Sánchez-Heras","full_name":"Sánchez-Heras, Ana Beatriz"},{"first_name":"Pilar","last_name":"Mur","full_name":"Mur, Pilar"},{"full_name":"Soto, José Luis","first_name":"José Luis","last_name":"Soto"},{"first_name":"Gemma","last_name":"Aiza","full_name":"Aiza, Gemma"},{"full_name":"Borràs, Emma","first_name":"Emma","last_name":"Borràs"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Alexey S.","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S."},{"last_name":"Bazykin","first_name":"Georgii A.","full_name":"Bazykin, Georgii A."},{"full_name":"Valle, Laura","last_name":"Valle","first_name":"Laura"}],"scopus_import":"1","page":"837-845","day":"01","article_type":"original","quality_controlled":"1","status":"public","abstract":[{"text":"Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.","lang":"eng"}],"date_created":"2024-05-05T22:01:04Z","file":[{"access_level":"open_access","creator":"dernst","date_updated":"2025-01-09T09:21:25Z","relation":"main_file","file_id":"18799","checksum":"e45fc987f4e9ebafdd0ec4f0e9027de4","file_size":3060724,"success":1,"file_name":"2024_EJHG_Andrianova.pdf","date_created":"2025-01-09T09:21:25Z","content_type":"application/pdf"}],"oa":1,"type":"journal_article"},{"month":"09","title":"Energies of dilute Fermi gases and universalities in BCS theory","ddc":["515","539"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11732"},{"id":"14542","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18107"},{"id":"17240","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14931"}]},"degree_awarded":"PhD","author":[{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard"}],"project":[{"name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"year":"2024","doi":"10.15479/at:ista:18135","day":"23","page":"353","status":"public","corr_author":"1","file":[{"relation":"main_file","access_level":"open_access","creator":"alaurits","date_updated":"2024-09-26T13:11:24Z","checksum":"c7bc3b31e430d57c65393051ca439575","file_size":3648831,"file_id":"18147","file_name":"Lauritsen-thesis-final.pdf","content_type":"application/pdf","date_created":"2024-09-26T13:11:24Z","success":1},{"file_name":"Lauritsen-thesis-source.zip","content_type":"application/x-zip-compressed","date_created":"2024-09-26T13:12:55Z","file_id":"18148","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","file_size":1625888,"access_level":"closed","creator":"alaurits","date_updated":"2024-09-26T13:12:55Z","relation":"source_file"}],"oa":1,"type":"dissertation","abstract":[{"text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$.","lang":"eng"}],"date_created":"2024-09-24T10:56:25Z","date_updated":"2026-04-16T08:17:55Z","article_processing_charge":"No","_id":"18135","OA_place":"publisher","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"citation":{"apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024."},"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"ec_funded":1,"oa_version":"Published Version","date_published":"2024-09-23T00:00:00Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"file_date_updated":"2024-09-26T13:12:55Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"issue":"7","_id":"14931","date_updated":"2026-04-16T08:17:56Z","article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Lauritsen, A. B., &#38; Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>, vol. 286, no. 7, 110320, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>.","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. 2024;286(7). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>.","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” <i>Journal of Functional Analysis</i>, vol. 286, no. 7. Elsevier, 2024."},"publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"department":[{"_id":"RoSe"}],"external_id":{"isi":["001170294000001"],"arxiv":["2301.04894"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","publication_status":"published","publisher":"Elsevier","date_published":"2024-04-01T00:00:00Z","volume":286,"ec_funded":1,"oa_version":"Published Version","file_date_updated":"2024-07-22T11:11:56Z","intvolume":"       286","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Journal of Functional Analysis","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","isi":1,"related_material":{"record":[{"id":"18135","relation":"dissertation_contains","status":"public"}]},"ddc":["510"],"title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","month":"04","day":"01","scopus_import":"1","author":[{"full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"year":"2024","doi":"10.1016/j.jfa.2024.110320","article_type":"original","article_number":"110320","corr_author":"1","status":"public","quality_controlled":"1","arxiv":1,"date_created":"2024-02-04T23:00:53Z","abstract":[{"lang":"eng","text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]."}],"type":"journal_article","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2024-07-22T11:11:56Z","relation":"main_file","file_id":"17305","checksum":"ee203cf2dc4420ad90d3c9970d246a78","file_size":1381063,"success":1,"file_name":"2024_JourFunctAnalysis_Lauritsen.pdf","content_type":"application/pdf","date_created":"2024-07-22T11:11:56Z"}],"oa":1},{"month":"01","title":"Decomposition of geometric graphs into star-forests","related_material":{"record":[{"relation":"later_version","status":"public","id":"21253"}]},"doi":"10.1007/978-3-031-49272-3_23","year":"2024","project":[{"call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"}],"author":[{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János","first_name":"János","last_name":"Pach"},{"last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza"},{"full_name":"Schnider, Patrick","first_name":"Patrick","last_name":"Schnider"}],"scopus_import":"1","page":"339-346","day":"01","quality_controlled":"1","arxiv":1,"status":"public","oa":1,"type":"conference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.13201"}],"abstract":[{"text":"We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs.","lang":"eng"}],"date_created":"2024-02-18T23:01:03Z","article_processing_charge":"No","date_updated":"2026-04-16T09:12:37Z","_id":"15012","language":[{"iso":"eng"}],"external_id":{"arxiv":["2306.13201"],"isi":["001207939600023"]},"department":[{"_id":"HeEd"}],"citation":{"ista":"Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346.","short":"J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346.","ama":"Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: <i>31st International Symposium on Graph Drawing and Network Visualization</i>. Vol 14465. Springer Nature; 2024:339-346. doi:<a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">10.1007/978-3-031-49272-3_23</a>","mla":"Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” <i>31st International Symposium on Graph Drawing and Network Visualization</i>, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:<a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">10.1007/978-3-031-49272-3_23</a>.","apa":"Pach, J., Saghafian, M., &#38; Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In <i>31st International Symposium on Graph Drawing and Network Visualization</i> (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">https://doi.org/10.1007/978-3-031-49272-3_23</a>","ieee":"J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in <i>31st International Symposium on Graph Drawing and Network Visualization</i>, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346.","chicago":"Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In <i>31st International Symposium on Graph Drawing and Network Visualization</i>, 14465:339–46. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">https://doi.org/10.1007/978-3-031-49272-3_23</a>."},"publication_identifier":{"eisbn":["9783031492723"],"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031492716"]},"oa_version":"Preprint","ec_funded":1,"date_published":"2024-01-01T00:00:00Z","volume":14465,"publisher":"Springer Nature","publication_status":"published","conference":{"start_date":"2023-09-20","name":"GD: Graph Drawing and Network Visualization","location":"Isola delle Femmine, Palermo, Italy","end_date":"2023-09-22"},"isi":1,"acknowledgement":"János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31.","alternative_title":["LNCS"],"publication":"31st International Symposium on Graph Drawing and Network Visualization","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"     14465"},{"volume":63,"date_published":"2024-10-01T00:00:00Z","oa_version":"Published Version","ec_funded":1,"publisher":"Springer Nature","publication_status":"published","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"acknowledgement":"Tobias Winkler and Joost-Pieter Katoen are supported by the DFG RTG 2236 UnRAVeL and the innovation programme under the Marie Skłodowska-Curie grant agreement No. 101008233 (Mission). Krishnendu Chatterjee is supported by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) Project ICT15-003. Maximilian Weininger is supported by the DFG projects 383882557 Statistical Unbounded Verification (SUV) and 427755713 Group-By Objectives in Probabilistic Verification (GOPro). Stefanie Mohr is supported by the DFG RTG 2428 CONVEY. Open Access funding enabled and organized by Projekt DEAL.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-01-09T07:31:31Z","intvolume":"        63","publication":"Formal Methods in System Design","_id":"12738","article_processing_charge":"Yes (via OA deal)","date_updated":"2026-04-16T09:31:13Z","has_accepted_license":"1","OA_place":"publisher","OA_type":"hybrid","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publication_identifier":{"eissn":["1572-8102"]},"citation":{"chicago":"Chatterjee, Krishnendu, Joost P Katoen, Stefanie Mohr, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Objectives.” <i>Formal Methods in System Design</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10703-023-00411-4\">https://doi.org/10.1007/s10703-023-00411-4</a>.","ieee":"K. Chatterjee, J. P. Katoen, S. Mohr, M. Weininger, and T. Winkler, “Stochastic games with lexicographic objectives,” <i>Formal Methods in System Design</i>, vol. 63. Springer Nature, pp. 40–80, 2024.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Objectives.” <i>Formal Methods in System Design</i>, vol. 63, Springer Nature, 2024, pp. 40–80, doi:<a href=\"https://doi.org/10.1007/s10703-023-00411-4\">10.1007/s10703-023-00411-4</a>.","ama":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. Stochastic games with lexicographic objectives. <i>Formal Methods in System Design</i>. 2024;63:40-80. doi:<a href=\"https://doi.org/10.1007/s10703-023-00411-4\">10.1007/s10703-023-00411-4</a>","ista":"Chatterjee K, Katoen JP, Mohr S, Weininger M, Winkler T. 2024. Stochastic games with lexicographic objectives. Formal Methods in System Design. 63, 40–80.","short":"K. Chatterjee, J.P. Katoen, S. Mohr, M. Weininger, T. Winkler, Formal Methods in System Design 63 (2024) 40–80.","apa":"Chatterjee, K., Katoen, J. P., Mohr, S., Weininger, M., &#38; Winkler, T. (2024). Stochastic games with lexicographic objectives. <i>Formal Methods in System Design</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10703-023-00411-4\">https://doi.org/10.1007/s10703-023-00411-4</a>"},"external_id":{"isi":["000946174300001"]},"status":"public","quality_controlled":"1","type":"journal_article","oa":1,"file":[{"file_id":"18781","checksum":"111e76b76163640a2c89237642af586f","file_size":2614190,"access_level":"open_access","creator":"dernst","date_updated":"2025-01-09T07:31:31Z","relation":"main_file","success":1,"file_name":"2024_FromMethodsSys_Chatterjee.pdf","date_created":"2025-01-09T07:31:31Z","content_type":"application/pdf"}],"date_created":"2023-03-19T23:00:59Z","abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies."}],"title":"Stochastic games with lexicographic objectives","month":"10","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"8272"}]},"ddc":["000"],"article_type":"original","page":"40-80","scopus_import":"1","day":"01","year":"2024","doi":"10.1007/s10703-023-00411-4","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P","last_name":"Katoen","first_name":"Joost P","orcid":"0000-0002-6143-1926"},{"last_name":"Mohr","first_name":"Stefanie","full_name":"Mohr, Stefanie"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"},{"first_name":"Tobias","last_name":"Winkler","full_name":"Winkler, Tobias"}]},{"OA_type":"gold","language":[{"iso":"eng"}],"OA_place":"publisher","has_accepted_license":"1","external_id":{"isi":["001142794000839"],"pmid":["38167818"]},"citation":{"short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169.","mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>, vol. 15, 169, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>","apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>","ieee":"M. Valentini <i>et al.</i>, “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>."},"publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"department":[{"_id":"GeKa"}],"date_updated":"2025-10-15T06:31:47Z","article_processing_charge":"Yes","_id":"14793","acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"Nature Communications","intvolume":"        15","file_date_updated":"2024-01-17T11:03:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"oa_version":"Published Version","volume":15,"date_published":"2024-01-02T00:00:00Z","publication_status":"published","publisher":"Springer Nature","APC_amount":"6468 EUR","article_number":"169","article_type":"original","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","last_name":"Valentini","first_name":"Marco"},{"first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"},{"first_name":"Levon","last_name":"Baghumyan","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","full_name":"Baghumyan, Levon"},{"first_name":"Thijs","last_name":"de Gijsel","id":"a0ece13c-b527-11ee-929d-bad130106eee","full_name":"de Gijsel, Thijs"},{"full_name":"Jung, Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","first_name":"Jason","last_name":"Jung"},{"last_name":"Calcaterra","first_name":"Stefano","full_name":"Calcaterra, Stefano"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L"},{"full_name":"Aggarwal, Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","first_name":"Kushagra","last_name":"Aggarwal"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","full_name":"Janik, Marian","orcid":"0009-0003-9037-8831","last_name":"Janik","first_name":"Marian"},{"first_name":"Thomas","last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","full_name":"Adletzberger, Thomas"},{"full_name":"Seoane Souto, Rubén","first_name":"Rubén","last_name":"Seoane Souto"},{"first_name":"Martin","last_name":"Leijnse","full_name":"Leijnse, Martin"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"},{"last_name":"Schrade","first_name":"Constantin","full_name":"Schrade, Constantin"},{"full_name":"Bakkers, Erik","first_name":"Erik","last_name":"Bakkers"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"project":[{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"},{"name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515"},{"_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811","grant_number":"101115315","name":"Quantum bits with Kitaev Transmons"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"doi":"10.1038/s41467-023-44114-0","year":"2024","day":"02","DOAJ_listed":"1","scopus_import":"1","month":"01","title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"file":[{"date_updated":"2024-01-17T11:03:00Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"14825","file_size":2336595,"checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","success":1,"content_type":"application/pdf","date_created":"2024-01-17T11:03:00Z","file_name":"2024_NatureComm_Valentini.pdf"}],"oa":1,"type":"journal_article","abstract":[{"lang":"eng","text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on  the same silicon technology compatible platform."}],"date_created":"2024-01-14T23:00:56Z","quality_controlled":"1","status":"public","corr_author":"1"},{"type":"journal_article","oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"file":[{"content_type":"application/pdf","date_created":"2024-12-03T08:56:53Z","file_name":"2024_PloSBio_Kim.pdf","success":1,"relation":"main_file","date_updated":"2024-12-03T08:56:53Z","access_level":"open_access","creator":"dernst","file_size":3057631,"checksum":"7de2dcb50deb65dde05c80082bb85a82","file_id":"18608"}],"date_created":"2024-12-01T23:01:54Z","abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the rodent hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}],"status":"public","quality_controlled":"1","corr_author":"1","article_type":"original","article_number":"e3002879","scopus_import":"1","day":"18","DOAJ_listed":"1","doi":"10.1371/journal.pbio.3002879","year":"2024","author":[{"full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim","orcid":"0000-0003-2344-1039"},{"id":"3337E116-F248-11E8-B48F-1D18A9856A87","full_name":"Okamoto, Yuji","last_name":"Okamoto","first_name":"Yuji","orcid":"0000-0003-0408-6094"},{"orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"project":[{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"name":"Structural & functional basis of presynaptic plasticity","_id":"b1b85715-d554-11ed-a5ad-84a07fc9f18e","grant_number":"I06166"},{"name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01205"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","month":"11","related_material":{"record":[{"id":"18296","relation":"research_data","status":"public"}]},"ddc":["570"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"acknowledgement":"We thank Carolina Borges-Merjane, Jing-Jing Chen, Katharina Lichter, and Samuel Young for critically reading the manuscript; the Electron Microscopy Facility of ISTA, in particular Vanessa Zheden, for extensive support, advice, and experimental assistance; the Preclinical Facility of ISTA, in particular Victoria Wimmer and Michael Schunn, for experimental assistance; Florian Marr and Christina Altmutter for technical support; Alois Schlögl for help with analysis; and Eleftheria Kralli-Beller for manuscript editing. We also thank Cordelia Imig for providing Munc13-1cKO-Munc13-2/3(−/−) mutant mice. Part of the work has been published in O.K.’s thesis in partial fulfillment of the requirements for the degree of Doctor of Philosophy.\r\nThis project received funding from the European Research Council and European Union’s Horizon 2020 research and innovation programme (ERC 692692 to P.J.; https://cordis.europa.eu/project/id/692692/de) and from the Fond zur Förderung der Wissenschaftlichen Forschung (Z312-B27 Wittgenstein award to P.J., https://www.fwf.ac.at/en/funding/portfolio/projects/fwf-wittgenstein-award; W1205-B09 and P36232-B to P.J., https://www.fwf.ac.at/en/funding; I6166-B to R.S.; https://www.fwf.ac.at/en/funding). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-12-03T08:56:53Z","intvolume":"        22","publication":"PLoS Biology","date_published":"2024-11-18T00:00:00Z","volume":22,"oa_version":"Published Version","ec_funded":1,"APC_amount":"6248,82 EUR","publisher":"Public Library of Science","publication_status":"published","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"OA_type":"gold","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"pmid":1,"publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"citation":{"apa":"Kim, O., Okamoto, Y., Kaufmann, W., Brose, N., Shigemoto, R., &#38; Jonas, P. M. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002879\">https://doi.org/10.1371/journal.pbio.3002879</a>","ama":"Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. <i>PLoS Biology</i>. 2024;22(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002879\">10.1371/journal.pbio.3002879</a>","mla":"Kim, Olena, et al. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” <i>PLoS Biology</i>, vol. 22, no. 11, e3002879, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002879\">10.1371/journal.pbio.3002879</a>.","ista":"Kim O, Okamoto Y, Kaufmann W, Brose N, Shigemoto R, Jonas PM. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. PLoS Biology. 22(11), e3002879.","short":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, P.M. Jonas, PLoS Biology 22 (2024).","chicago":"Kim, Olena, Yuji Okamoto, Walter Kaufmann, Nils Brose, Ryuichi Shigemoto, and Peter M Jonas. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002879\">https://doi.org/10.1371/journal.pbio.3002879</a>.","ieee":"O. Kim, Y. Okamoto, W. Kaufmann, N. Brose, R. Shigemoto, and P. M. Jonas, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons,” <i>PLoS Biology</i>, vol. 22, no. 11. Public Library of Science, 2024."},"external_id":{"isi":["001358568700003"],"pmid":["39556620"]},"_id":"18603","article_processing_charge":"Yes","date_updated":"2026-04-16T12:20:34Z","issue":"11"},{"type":"research_data","file":[{"success":1,"date_created":"2024-10-11T10:04:19Z","content_type":"application/zip","file_name":"Kim_et_al_2024_PlosBio_Source_data.zip","file_id":"18297","file_size":164382,"checksum":"0a977e7df54c418251b10dfd3f8a015c","date_updated":"2024-10-11T10:04:19Z","access_level":"open_access","creator":"okim","relation":"main_file"},{"file_name":"info.txt","date_created":"2024-10-11T10:04:23Z","content_type":"text/plain","success":1,"checksum":"5b9343d6b2035ac3185e390fad4d3830","file_size":654,"file_id":"18298","relation":"main_file","access_level":"open_access","creator":"okim","date_updated":"2024-10-11T10:04:23Z"}],"oa":1,"keyword":["Hippocampal mossy fiber synapses","short-term potentiation","long-term potentiation","presynaptic plasticity","electron microscopy","freeze-fracture replica labeling","paired recordings","forskolin","cyclic adenosine monophosphate (cAMP)","protein kinase A (PKA)","neuromodulation","synaptic vesicle pools","presynaptic Ca2+ channels","Munc13","docking","priming","active zone"],"date_created":"2024-10-11T10:12:17Z","abstract":[{"text":"It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.","lang":"eng"}],"status":"public","corr_author":"1","contributor":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Kim","first_name":"Olena"},{"contributor_type":"researcher","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","first_name":"Yuji","last_name":"Okamoto"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","contributor_type":"researcher","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nils ","last_name":"Brose","contributor_type":"researcher"},{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","contributor_type":"researcher","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804"}],"day":"11","doi":"10.15479/AT:ISTA:18296","year":"2024","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"}],"author":[{"full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","last_name":"Kim","first_name":"Olena","orcid":"0000-0003-2344-1039"}],"title":"Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons","month":"10","related_material":{"record":[{"id":"18603","relation":"used_in_publication","status":"public"}]},"ddc":["570"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","file_date_updated":"2024-10-11T10:04:23Z","date_published":"2024-10-11T00:00:00Z","oa_version":"Submitted Version","ec_funded":1,"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","department":[{"_id":"PeJo"},{"_id":"RySh"},{"_id":"EM-Fac"}],"citation":{"ama":"Kim O. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>","mla":"Kim, Olena. <i>Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","short":"O. Kim, (2024).","ista":"Kim O. 2024. Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">10.15479/AT:ISTA:18296</a>.","apa":"Kim, O. (2024). Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>","chicago":"Kim, Olena. “Presynaptic CAMP-PKA-Mediated Potentiation Induces Reconfiguration of Synaptic Vesicle Pools and Channel-Vesicle Coupling at Hippocampal Mossy Fiber Boutons.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:18296\">https://doi.org/10.15479/AT:ISTA:18296</a>.","ieee":"O. Kim, “Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons.” Institute of Science and Technology Austria, 2024."},"_id":"18296","article_processing_charge":"No","date_updated":"2026-04-16T12:20:33Z"},{"ddc":["530"],"month":"04","title":"Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck","year":"2024","doi":"10.5194/mr-5-33-2024","author":[{"last_name":"Napoli","first_name":"Federico","orcid":"0000-0002-9043-136X","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","full_name":"Napoli, Federico"},{"first_name":"Jia-Ying","last_name":"Guan","full_name":"Guan, Jia-Ying"},{"first_name":"Charles-Adrien","last_name":"Arnaud","full_name":"Arnaud, Charles-Adrien"},{"full_name":"Macek, Pavel","last_name":"Macek","first_name":"Pavel"},{"full_name":"Fraga, Hugo","last_name":"Fraga","first_name":"Hugo"},{"first_name":"Cécile","last_name":"Breyton","full_name":"Breyton, Cécile"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"}],"project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"scopus_import":"1","page":"33-49","day":"19","article_type":"original","corr_author":"1","quality_controlled":"1","status":"public","abstract":[{"text":"Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with a H2O-based culture medium doped with deuterated cell lysate allow scientists to overcome this “reprotonation bottleneck” while retaining a high level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence lifetimes of several proteins prepared with this labeling pattern over a range of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range, many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and we show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments.","lang":"eng"}],"date_created":"2024-05-16T15:02:43Z","acknowledged_ssus":[{"_id":"NMR"}],"oa":1,"file":[{"success":1,"date_created":"2024-05-22T07:01:15Z","content_type":"application/pdf","file_name":"2024_MagneticResonance_Napoli.pdf","file_id":"15413","file_size":6657865,"checksum":"80ea50114e428461ca9530d3bd5d89e4","date_updated":"2024-05-22T07:01:15Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"type":"journal_article","issue":"1","article_processing_charge":"Yes","date_updated":"2025-07-17T08:12:23Z","_id":"15401","external_id":{"pmid":["40384771"]},"pmid":1,"department":[{"_id":"PaSc"}],"citation":{"ieee":"F. Napoli <i>et al.</i>, “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024.","chicago":"Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>.","ista":"Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 5(1), 33–49.","short":"F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49.","ama":"Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. 2024;5(1):33-49. doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>","mla":"Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>.","apa":"Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C., &#38; Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>"},"publication_identifier":{"issn":["2699-0016"]},"has_accepted_license":"1","OA_type":"gold","language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"Copernicus Publications","publication_status":"published","APC_amount":"1530 EUR","oa_version":"Published Version","volume":5,"date_published":"2024-04-19T00:00:00Z","publication":"Magnetic Resonance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-05-22T07:01:15Z","intvolume":"         5","acknowledgement":"We thank Dominique Madern (IBS Grenoble) for providing the plasmid for MalDH and feedback on the article, Alicia Vallet for excellent support at the Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of Max Perutz Labs for the mass spectrometry analysis using the instruments of the Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University Dortmund) for sharing a paper draft describing a similar study. This work was supported by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis (Lyon) and the reviewers for constructive input.\r\nThis research has been supported by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien Arnaud was funded by GRAL.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}}]